############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:methodical.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings methodical_1.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/methodical.Rcheck’ * using R version 4.4.0 RC (2024-04-16 r86468) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘methodical/DESCRIPTION’ ... OK * this is package ‘methodical’ version ‘1.1.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘methodical’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: ‘HDF5Array:::.serialize_HDF5SummarizedExperiment’ See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘.chunk_regions’ ‘.tss_iterator’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .calculate_regions_intersections: no visible global function definition for ‘is’ .chunk_regions: no visible global function definition for ‘is’ .chunk_regions: no visible global function definition for ‘subsetByOverlaps’ .count_covered_bases: no visible global function definition for ‘is’ .create_meth_rse_from_hdf5: no visible global function definition for ‘setNames’ .split_bedgraph: no visible binding for global variable ‘meth_site_groups’ .split_bedgraph: no visible binding for global variable ‘total_files’ .split_bedgraph: no visible binding for global variable ‘meth_sites_df’ .split_bedgraph: no visible global function definition for ‘setNames’ .split_bedgraph: no visible binding for global variable ‘seqnames_column’ .split_bedgraph: no visible binding for global variable ‘start_column’ .split_bedgraph: no visible binding for global variable ‘end_column’ .split_bedgraph: no visible binding for global variable ‘value_column’ .split_bedgraph: no visible binding for global variable ‘dt_threads’ .split_bedgraph: no visible binding for global variable ‘zero_based’ .split_bedgraph: no visible binding for global variable ‘normalization_factor’ .split_bedgraph: no visible binding for global variable ‘decimal_places’ .split_bedgraph: no visible binding for global variable ‘mg’ .split_bedgraph: no visible binding for global variable ‘temp_chunk_dirs’ .split_meth_array_file: no visible binding for global variable ‘probe_groups’ .split_meth_array_file: no visible binding for global variable ‘total_files’ .split_meth_array_file: no visible binding for global variable ‘probe_sites_df’ .split_meth_array_file: no visible global function definition for ‘setNames’ .split_meth_array_file: no visible binding for global variable ‘probe_name_column’ .split_meth_array_file: no visible binding for global variable ‘beta_value_column’ .split_meth_array_file: no visible binding for global variable ‘normalization_factor’ .split_meth_array_file: no visible binding for global variable ‘decimal_places’ .split_meth_array_file: no visible binding for global variable ‘name’ .split_meth_array_file: no visible binding for global variable ‘pg’ .split_meth_array_file: no visible binding for global variable ‘temp_chunk_dirs’ .split_meth_array_file: no visible binding for global variable ‘dt_threads’ .split_meth_array_files_into_chunks: no visible binding for global variable ‘name’ .summarize_chunk_methylation: no visible global function definition for ‘subsetByOverlaps’ .tss_correlations: no visible global function definition for ‘setNames’ .write_chunks_to_hdf5: no visible binding for global variable ‘chunk’ annotateGRanges: no visible global function definition for ‘is’ annotatePlot: no visible global function definition for ‘is’ annotatePlot: no visible global function definition for ‘colorRampPalette’ annotatePlot: no visible global function definition for ‘subsetByOverlaps’ annotatePlot: no visible binding for global variable ‘region_type’ calculateMethSiteTranscriptCors: no visible global function definition for ‘is’ calculateMethSiteTranscriptCors: no visible binding for global variable ‘chunk’ calculateMethSiteTranscriptCors: no visible global function definition for ‘subsetByOverlaps’ calculateMethSiteTranscriptCors: no visible global function definition for ‘setNames’ calculateRegionMethylationTranscriptCors: no visible global function definition for ‘is’ calculateRegionMethylationTranscriptCors: no visible binding for global variable ‘p.adjust.methods’ calculateRegionMethylationTranscriptCors : : no visible global function definition for ‘setNames’ calculateRegionMethylationTranscriptCors: no visible global function definition for ‘p.adjust’ calculateSmoothedMethodicalScores: no visible global function definition for ‘is’ createRandomRegions: no visible global function definition for ‘is’ createRandomRegions: no visible global function definition for ‘seqlengths’ createRandomRegions: no visible global function definition for ‘overlapsAny’ extractGRangesMethSiteValues: no visible global function definition for ‘is’ extractMethSitesFromGenome: no visible global function definition for ‘is’ findTMRs: no visible global function definition for ‘is’ kallistoIndex: no visible global function definition for ‘is’ kallistoQuantify: no visible global function definition for ‘is’ kallistoQuantify: no visible global function definition for ‘setNames’ liftoverMethRSE: no visible global function definition for ‘is’ makeMethRSEFromArrayFiles: no visible global function definition for ‘is’ makeMethRSEFromBedgraphs: no visible global function definition for ‘is’ maskRangesInRSE: no visible global function definition for ‘is’ maskRangesInRSE: no visible global function definition for ‘queryHits’ methrixToRSE: no visible global function definition for ‘is’ plotMethSiteCorCoefs: no visible global function definition for ‘is’ plotMethSiteCorCoefs: no visible binding for global variable ‘cor’ plotMethSiteCorCoefs: no visible global function definition for ‘complete.cases’ plotMethSiteCorCoefs: no visible binding for global variable ‘meth_cor_plot_position’ plotMethodicalScores: no visible global function definition for ‘is’ plotMethodicalScores: no visible global function definition for ‘seqlevels’ plotMethodicalScores: no visible binding for global variable ‘meth_site_start’ plotMethodicalScores: no visible binding for global variable ‘meth_site_plot_position’ plotMethodicalScores: no visible binding for global variable ‘methodical_score’ plotMethodicalScores: no visible binding for global variable ‘cor’ plotMethylationValues: no visible global function definition for ‘is’ plotMethylationValues: no visible global function definition for ‘complete.cases’ plotMethylationValues: no visible binding for global variable ‘meth_site_plot_position’ plotTMRs: no visible global function definition for ‘is’ plotTMRs: no visible binding for global variable ‘direction’ plotTMRs: no visible global function definition for ‘setNames’ rangesRelativeToTSS: no visible global function definition for ‘is’ rapidCorTest: no visible global function definition for ‘is’ rapidCorTest: no visible binding for global variable ‘p.adjust.methods’ rapidCorTest: no visible global function definition for ‘cor’ rapidCorTest: no visible global function definition for ‘pt’ rapidCorTest: no visible global function definition for ‘p.adjust’ sampleMethSites: no visible global function definition for ‘is’ strandedDistance: no visible global function definition for ‘is’ sumTranscriptValuesForGenes: no visible global function definition for ‘is’ sumTranscriptValuesForGenes : : no visible global function definition for ‘is’ sumTranscriptValuesForGenes: no visible binding for global variable ‘gene_transcripts’ summarizeRegionMethylation: no visible global function definition for ‘is’ summarizeRegionMethylation: no visible global function definition for ‘seqlevels’ Undefined global functions or variables: beta_value_column chunk colorRampPalette complete.cases cor decimal_places direction dt_threads end_column gene_transcripts is meth_cor_plot_position meth_site_groups meth_site_plot_position meth_site_start meth_sites_df methodical_score mg name normalization_factor overlapsAny p.adjust p.adjust.methods pg probe_groups probe_name_column probe_sites_df pt queryHits region_type seqlengths seqlevels seqnames_column setNames start_column subsetByOverlaps temp_chunk_dirs total_files value_column zero_based Consider adding importFrom("grDevices", "colorRampPalette") importFrom("methods", "is") importFrom("stats", "complete.cases", "cor", "p.adjust", "p.adjust.methods", "pt", "setNames") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE checkRd: (-1) kallistoQuantify.Rd:34: Lost braces; missing escapes or markup? 34 | {merged_output_prefix}_counts_merged.tsv.gz and {merged_output_prefix}_tpm_merged.tsv.gz. Default prefix is "kallisto_transcript" i.e. default output merged output files are | ^ checkRd: (-1) kallistoQuantify.Rd:34: Lost braces; missing escapes or markup? 34 | {merged_output_prefix}_counts_merged.tsv.gz and {merged_output_prefix}_tpm_merged.tsv.gz. Default prefix is "kallisto_transcript" i.e. default output merged output files are | ^ * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed extractMethSitesFromGenome 133.990 13.892 147.885 liftoverMethRSE 100.607 11.652 112.818 annotateGRanges 35.766 3.091 43.723 makeMethRSEFromBedgraphs 9.021 9.064 9.582 makeMethRSEFromArrayFiles 11.703 3.725 12.474 summarizeRegionMethylation 8.260 3.436 11.504 calculateMethSiteTranscriptCors 9.130 0.584 9.627 calculateRegionMethylationTranscriptCors 6.417 1.171 7.529 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/methodical.Rcheck/00check.log’ for details.